https://github.com/OHDSI/CohortMethod
An R package for performing new-user cohort studies in an observational database in the OMOP Common Data Model.
https://github.com/OHDSI/CohortMethod
hades
Last synced: 4 months ago
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An R package for performing new-user cohort studies in an observational database in the OMOP Common Data Model.
- Host: GitHub
- URL: https://github.com/OHDSI/CohortMethod
- Owner: OHDSI
- Created: 2014-06-12T16:30:07.000Z (almost 11 years ago)
- Default Branch: main
- Last Pushed: 2024-10-24T19:04:51.000Z (6 months ago)
- Last Synced: 2024-10-26T05:21:49.623Z (6 months ago)
- Topics: hades
- Language: R
- Homepage: https://ohdsi.github.io/CohortMethod
- Size: 115 MB
- Stars: 82
- Watchers: 50
- Forks: 57
- Open Issues: 13
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
Awesome Lists containing this project
- jimsghstars - OHDSI/CohortMethod - An R package for performing new-user cohort studies in an observational database in the OMOP Common Data Model. (R)
README
CohortMethod
============
[](https://github.com/OHDSI/CohortMethod/actions?query=workflow%3AR-CMD-check)
[](https://codecov.io/github/OHDSI/CohortMethod?branch=main)
CohortMethod is part of [HADES](https://ohdsi.github.io/Hades).
Introduction
============
CohortMethod is an R package for performing new-user cohort studies in an observational database in the OMOP Common Data Model.
Features
========
- Extracts the necessary data from a database in OMOP Common Data Model format.
- Uses a large set of covariates for both the propensity and outcome model, including for example all drugs, diagnoses, procedures, as well as age, comorbidity indexes, etc.
- Large scale regularized regression to fit the propensity and outcome models.
- Includes function for trimming, stratifying, matching, and weighting on propensity scores.
- Includes diagnostic functions, including propensity score distribution plots and plots showing covariate balance before and after matching and/or trimming.
- Supported outcome models are (conditional) logistic regression, (conditional) Poisson regression, and (conditional) Cox regression.
Screenshots
===========
Propensity (preference score) distributionCovariate balance plot
Technology
============
CohortMethod is an R package, with some functions implemented in C++.
System Requirements
============
Requires R (version 3.6.0 or higher). Installation on Windows requires [RTools](https://cran.r-project.org/bin/windows/Rtools/). Libraries used in CohortMethod require Java.
Installation
=============
1. See the instructions [here](https://ohdsi.github.io/Hades/rSetup.html) for configuring your R environment, including RTools and Java.
2. In R, use the following commands to download and install CohortMethod:
```r
install.packages("remotes")
remotes::install_github("ohdsi/CohortMethod")
```
3. Optionally, run this to check if CohortMethod was correctly installed:
```r
connectionDetails <- createConnectionDetails(dbms="postgresql",
server="my_server.org",
user = "joe",
password = "super_secret")
checkCmInstallation(connectionDetails)
```
Where dbms, server, user, and password need to be changed to the settings for your database environment. Type
```r
?createConnectionDetails
```
for more details on how to configure your database connection.
User Documentation
==================
Documentation can be found on the [package website](https://ohdsi.github.io/CohortMethod).
PDF versions of the documentation are also available:
* Vignette: [Single studies using the CohortMethod package](https://raw.githubusercontent.com/OHDSI/CohortMethod/main/inst/doc/SingleStudies.pdf)
* Vignette: [Running multiple analyses at once using the CohortMethod package](https://raw.githubusercontent.com/OHDSI/CohortMethod/main/inst/doc/MultipleAnalyses.pdf)
* Package manual: [CohortMethod.pdf](https://raw.githubusercontent.com/OHDSI/CohortMethod/main/extras/CohortMethod.pdf)
Support
=======
* Developer questions/comments/feedback: OHDSI Forum
* We use the GitHub issue tracker for all bugs/issues/enhancements
Contributing
============
Read [here](https://ohdsi.github.io/Hades/contribute.html) how you can contribute to this package.
License
=======
CohortMethod is licensed under Apache License 2.0
Development
===========
CohortMethod is being developed in R Studio.
### Development status
CohortMethod is actively being used in several studies and is ready for use.
# Acknowledgements
- This project is supported in part through the National Science Foundation grant IIS 1251151.